Large crowds protested in Hong Kong on Sunday after a pro-Beijing official was appointed to a senior role at the main university, as fears grow over what critics see as political interference in the city's education system.

The downtown rally staged by teachers, students and alumni comes in the wake of Arthur Li's selection last month as chairman of HKU's governing council.

The appointment taps in to wider concerns that academic freedoms in the city are under threat, particularly in the wake of last year's student-led mass pro-democracy rallies.

Demonstrators Sunday marched to the Government House, the residence of unpopular Hong Kong leader Leung Chun-ying, who appointed Li.

The protesters held banners that read "defend the university's autonomy" and "uphold academic freedom". Others shouted "Arthur Li, you will pay."

Organisers said 3,000 people took part in the protest, while police estimated the crowd at around 800.

Li, a member of Hong Kong's Executive Council, the top advisory body to the government, started his three-year term on January 1.

He is widely known to be close to Leung, who is also the chancellor of all the city's universities.

"The appointment is not just about HKU, it's not just about universities. This is an issue of governance in all of Hong Kong," Benny Tai, a key figure in last year's pro-democracy movement, told the crowd.

"The government just does not listen to public opinion," added Tai, who also teaches at the school.

Protester Timothy O'Leary, a humanities professor at HKU, told local broadcaster Cable TV: "I think this is a disappointing appointment. I think this is an indication that the government does not want to move forward in helping."

Li's appointment comes after the university's council, criticised as being pro-Beijing, rejected liberal law scholar Johannes Chan as pro-vice chancellor at the university, sparking protests from staff and students.

At a non-binding vote in November by HKU alumni on whether Li should be appointed, 98 percent said no.

The Hong Kong government defended the appointment Sunday.

"The decisions are based on the merits of individuals, including their ability, expertise, experience, integrity and commitment to public service," a government spokesman said in a statement.

Former British colony Hong Kong was handed back to China in 1997 under a deal that guaranteed the retention of its civil liberties and capitalist system for 50 years.

Teachers have previously accused officials of politically motivated censorship, including in 2012 when tens of thousands marched against "national education", a government proposal to introduce Beijing-centric patriotic teaching into schools. The plan was later dropped.